I am on a Cruise stopping at Hong Kong then visiting Shanghai, do I need a separate Visa for both?

John, as for HK, you don’t need it because you are Australian passport holder and you can enjoy free entry there.
In this way, you just need an entry permit to Shanghai.
But if you just transit in Shanghai for less than 24 hours and then go to a third country or region, you have a chance to enjoy free transit.